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Forensic Science International: Genetics
Forensic Science International: Genetics
A R T I C L E I N F O A B S T R A C T
Article history: We analyzed haplotypes for 22 Y chromosomal STRs (Y-STRs), including 17 Yfiler loci (DYS19, DYS385a/
Received 6 August 2013 b, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DY438, DYS439, DYS448, DYS456, DYS458,
Received in revised form 3 March 2014 DYS635 and Y-GATA-H4) and five additional STRs (DYS388, DYS446, DYS447, DYS449 and DYS464), and
Accepted 4 March 2014
Y chromosomal haplogroup distribution in 270 unrelated individuals from the Pathans residing in the
Federally Administered Tribal Areas and the North-West Frontier Province of Pakistan using in-house
Keywords: multiplex PCR systems. Each Y-STR showed diversities ranging from 0.2506 to 0.8538, and the
Y chromosome
discriminatory capacity (DC) was 73.7% with 199 observed haplotypes using 17 Yfiler loci. By the
Y-STR
Haplotype
addition of 5 Y-STRs to the Yfiler system, the DC was increased to 85.2% while showing 230 observed
Haplogroup haplotypes. Among the additional 5 Y-STRs, DYS446, DYS447 and DYS449 were major contributors to
Pathans enhancing discrimination. In the analysis of molecular variance, the Pathans of this study showed
Pakistan significant differences from other Pathan populations as well as neighboring population sets. In Y-SNP
analysis, a total of 12 Y chromosomal haplogroups were observed and the most frequent haplogroup was
R1a1a with 49.3% frequency. To obtain insights on the origin of Pathans, the network analysis was
performed for the haplogroups G and Q observed from the Pathans and the Jewish population groups
including Ashkenazim and Sephardim, but little support for a Jewish origin could be found. In the present
study, we report Y-STR population data in Pathans of Pakistan, and we emphasize the need for adding
additional markers to the commonly used 17 Yfiler loci to achieve more improved discriminatory
capacity in a population with low genetic diversity.
ß 2014 Elsevier Ireland Ltd. All rights reserved.
http://dx.doi.org/10.1016/j.fsigen.2014.03.004
1872-4973/ß 2014 Elsevier Ireland Ltd. All rights reserved.
112 E.Y. Lee et al. / Forensic Science International: Genetics 11 (2014) 111–116
Here, we report Y chromosomal haplogroups and haplotypes for DYS437, DY438, DYS439, DYS448, DYS456, DYS458, DYS635 and
22 Y-STRs including 17 Yfiler loci and 5 additional Y-STRs (DYS388, Y-GATA-H4) and 5 additional Y-STRs (DYS388, DYS446, DYS447,
DYS446, DYS447, DYS449 and DYS464) in 270 Pathan individuals DYS449 and DYS464) were amplified using three in-house
from Pakistan, and we investigate the relationship between the multiplex PCR systems as previously described [15]. The PCR
Pathans and historically or geographically relevant populations. products were separated by capillary electrophoresis using an ABI
PRISM 310 genetic Analyzer (Applied Biosystems). A peak
2. Materials and methods detection threshold of 100 RFU was used for allele designation
using GeneMapper ID Software versions 3.2 (Applied Biosystems)
2.1. DNA samples and each allele call at all STR loci was determined by comparing to
an allelic ladder. To ensure correct allele calls, Y-STR typing results
Blood samples were obtained from 270 unrelated male Pathans for more than 100 Pathan samples and the 9948 male control DNA
residing in the North West Frontier Province (NWFP) and the (Promega Corporations, Madison, MI, USA) were confirmed to be
Federally Administered Tribal Areas (FATA) of Pakistan. All comparable with the AmpFlSTR1 YfilerTM kit (Applied Biosystems,
participants gave their informed consent orally or in writing after Foster City, CA, USA).
one of the authors explained the aims and procedures of the study,
which was approved by The Institutional Review Board of 2.3. Y chromosomal haplogroup determination
Severance Hospital, Yonsei University in Seoul, Korea. DNA was
extracted using a QIAamp DNA mini kit (Qiagen, Hilden, Germany) The 19 biallelic Y chromosomal markers (M40, RPS4Y711, M89,
according to the manufacturer’s instructions. M201, M69, M304, M172, M9, M20, M175, M122, M45, M242,
M207, P231, M17, M479, M124 and M184) were selected to
2.2. Multiplex PCR and genotyping for 22 Y-STRs determine Y chromosomal haplogroups E, C, F, G, H, J, J2, K, L, O, O3,
P, Q, R, R1, R1a1a, R2, R2a and T, that are present in Eurasian
To define genotypes of 22 Y-STRs, 17 Yfiler loci (DYS19, populations (Fig. 1). All but M172 marker that was analyzed by
DYS385a/b, DYS389I/II, DYS390, DYS391, DYS392, DYS393, direct sequencing were analyzed using in-house multiplex PCR and
Fig. 1. Phylogenetic tree of the 19 Y chromosomal binary polymorphisms analyzed in this study. The SNPs are indicated in each branch and the haplogroups are indicated at
the end of each branch according to Karafet et al. [38]. The number of haplotypes of each haplogroup was compared in two different combinations of Y-STRs.
E.Y. Lee et al. / Forensic Science International: Genetics 11 (2014) 111–116 113
SBE reaction. The detailed methods for determination of Y data for 17 Yfiler loci has been deposited in the YHRD (Accession
chromosomal haplogroup are described in the Supplementary number YA003846). The locus or haplotype diversity (h) and the
Material. number of observed alleles or haplotypes for 19 single copy STR
loci and 2 multi-copy STRs are summarized in Supplementary
2.4. Statistical analysis Material Tables S2 and S3. Among single copy loci, the DYS449
showed the highest diversity of 0.8339, and the DYS388 was the
The following formulas were used: (1) discriminatory capaci- least diverse locus (h = 0.2506) with seven different alleles. The 2
ty = no. of different haplotypes/no. of individuals; (2) multi-copy Y-STRs, DYS385 and DYS464, were more diverse than
P
locus or haplotype diversity ¼ ½n=ðn 1Þ ð1 Pi2 , where Pi most of the single copy Y-STRs with diversity values of 0.8538 and
is the frequency of the ith allele or haplotype and n indicates 0.8258, respectively.
the number of individuals [16]. To examine the relationship
between neighboring populations, pair-wise genetic distances 3.2. Haplotype resolution with additional Y-STRs
(Fst) and associated probability values (p-values, 10,000 permuta-
tions) were calculated using the analysis of molecular variance We evaluated the haplotype resolution of variously combined
(AMOVA), which is available on the YHRD website [7]. The Pathan Y-STRs (Table 1). The discriminatory capacity (DC) of the 17 Yfiler
population of the present study was compared with the loci was 73.7% with 199 different haplotypes. By the addition of 5
Afghanistan Pathans (YHRD accession number YA003701), North Y-STRs (DYS388, DYS446, DYS447, DYS449 and DYS464) to the 17
Afghanistan Pathans (YA003703), South Afghanistan Pathans Yfiler loci, an improved discrimination capacity was obtained as a
(YA003702), Afridi Pathans in India (YA003686), Yousafzai Pathans DC of 85.2% from 230 observed haplotypes in 270 Pathan samples.
in Pakistan (YA003748) and full population sets, including 483 We investigated the change in haplotype diversity (h) and DC by
haplotypes from Afghanistan [7,13,14], 2068 haplotypes from adding 5 Y-STRs to the Yfiler loci. In the case of adding one Y-STR to
India [7,10,17–19], 703 haplotypes from Iran [7,20] and 1089 the Yfiler loci, DYS449 showed the greatest increase in DC and h,
haplotypes from Pakistan [7] based on the genotyping results for which were 78.5% and 0.9939, respectively. The improvement
15 Y-STR loci (DYS19, DYS389I/II, DYS390, DYS391, DYS392, achieved by DYS449 was followed by improvements with DYS446,
DYS393, DYS437, DY438, DYS439, DYS448, DYS456, DYS458, DYS464 and DYS447. Since DYS449 contributed the most to
DYS635 and Y-GATA-H4). increasing haplotype diversity, we then calculated the cumulative
In addition, genealogical relationships among haplotypes of the DC and h after the addition of other Y-STR to 18 loci, including
Pathan population and Jewish populations [21,22] within hap- Yfiler loci and DYS449. The DC value increased with the addition of
logroups G and Q were reconstructed using the program Network DYS446, DYS464 and DYS447, but did not change by the addition of
4.6.1.1 [23]. Since all haplotypes overlap in only 8 Y-STR loci DYS388. When 3 loci were added to Yfiler loci, the combination of
(DYS19, DYS388, DYS389I/b, DYS390, DYS391, DYS392 and DYS446, DYS447 and DYS449 was the most effective in increasing
DYS393), the 8 loci were used for the analysis, and the weighting the discrimination capacity. The combination of 5 additional Y-
scheme took into account the Y-STR variation across the STRs with the 17 Yfiler loci increased the h and DC to 0.9968 and
haplogroup as described in a previous report [24]. AMOVA and 85.2%, respectively.
Fst analysis were also performed for haplotypes of Pathans and In addition, we examined the change in haplotype resolution
Jewish populations using Arlequin software Version 3.5.1.2 with two different combinations of Y-STR loci (Table 2). Using 17
[21,22,25]. Yfiler loci, only 169 haplotypes (62.6%) were observed once and the
most frequent haplotype was shared by 23 individuals. By adding 5
3. Results additional Y-STRs to the Yfiler loci, 211 haplotypes were observed
once, which accounted for 78.1% of the total observed haplotypes.
3.1. Diversity of 22 Y-STRs The most frequent haplotype was shared by 12 individuals, and
their unrelatedness was confirmed by the analysis of autosomal
We could successfully obtain genotypes of total 22 Y-STRs from STRs and mitochondrial DNA (mtDNA) control region sequence
270 male individuals in a Pathan population except for one (PK- (data not shown). The shared haplotypes by Yfiler loci were
164) which showed a null allele at two adjacent loci, DYS458 and separated to more distinct haplotypes by key markers, as indicated
DYS449 (Supplementary Material Table S1), and the haplotype in Supplementary Material Table S4. It was clear that the additional
Table 1
Number of haplotypes and haplotype diversities for each combined Y-STRs in 270 Pathan samples.
Haplotype Diversitya No. of haplotypes No. of unique haplotypesb Discriminatory capacity (%) Haplotype diversity
underestimated. Nonetheless, DYS464 shows high diversity and In addition, the high frequencies of the South Asian hap-
has been considered to be a useful discriminative marker, only that logroups, H, L, R1a1a and R2a (67.4%) and the low frequencies of
the selection of DYS464 for forensic application must be made with the Middle Eastern haplogroups G, J and T (25.2%) were not
caution since the interpretation of profiles can be ambiguous when consistent with the results of mtDNA study in the same population
it comes to male-male admixed specimens or degraded DNA group [36], where the high frequency of the West Eurasian lineages
[32,33]. In the present study, because DYS464 showed a similar (55.6%) and the relatively low frequency of the South Asian
pattern with DYS446 or DYS449 in differentiation of haplotypes, lineages (39.1%) were observed. Therefore, further analyses of
the combination of DYS464 with DYS446 or DYS449 did not other loci with more samples would be helpful to elucidate the
increase haplotype diversity despite its high diversity and the population history of the Pathans.
presence of various alleles. On the other hand, DYS447 showed a
different pattern from other loci and its addition to Yfiler loci Conflict of interest
allowed for more diverse haplotypes in spite of its low gene
diversity. The authors declare that they have no conflict of interest.
After evaluation of the usefulness of additional markers, we
selected 3 Y-STR loci, DYS446, DYS447 and DYS449, that were Acknowledgements
effective Y-STRs to increase discriminatory capacity in the Pathan
population, while DYS388 and DYS464 were excluded due to the This research was supported by the Future-based Technology
low discrimination capacity or possible difficulty in interpretation. Development Program through the National Research Foundation
The low diversity of DYS388 in Pathans has also been reported in a of Korea (NRF) funded by the Ministry of Education, Science and
previous report [9]. The combination of these 3 Y-STRs with Yfiler Technology (nos. 2010-0020631 and 2011-0027729). The authors
loci drew a DC of 84.1% which was greatly improved but still at a would like to thank Mian Sahib Zar (Center of Excellence in
lower level compared to other population data. Therefore, further Molecular Biology, University of the Punjab, Pakistan) for his
investigation into other markers is needed to achieve more valuable comments on the Pathans.
discrimination in the Pathans, and RM Y-STRs may be good
candidates since they present high differentiation capacity even in
the same male lineage [29,30]. When we compared population Appendix A. Supplementary data
differentiation, Pakistani Pathans showed a significant difference
from other Pathan populations as well as from neighboring Supplementary data associated with this article can be found, in
population sets, which suggests the need to construct their own Y- the online version, at doi:10.1016/j.fsigen.2014.03.004.
STR database.
In Y-SNP analysis, the distribution of haplogroups showed a
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